Space pruning monotonic search for the non-unique probe selection problem Online publication date: Wed, 22-Oct-2014
by Elisa Pappalardo; Beyza Ahlatcioglu Ozkok; Panos M. Pardalos
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 10, No. 1, 2014
Abstract: Identification of targets, generally viruses or bacteria, in a biological sample is a relevant problem in medicine. Biologists can use hybridisation experiments to determine whether a specific DNA fragment, that represents the virus, is presented in a DNA solution. A probe is a segment of DNA or RNA, labelled with a radioactive isotope, dye or enzyme, used to find a specific target sequence on a DNA molecule by hybridisation. Selecting unique probes through hybridisation experiments is a difficult task, especially when targets have a high degree of similarity, for instance in a case of closely related viruses. After preliminary experiments, performed by a canonical Monte Carlo method with Heuristic Reduction (MCHR), a new combinatorial optimisation approach, the Space Pruning Monotonic Search (SPMS) method, is introduced. The experiments show that SPMS provides high quality solutions and outperforms the current state-of-the-art algorithms.
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